gene_x 0 like s 516 view s
Tags: plot, packages, R
Download the file typing_189.csv
library(ggtree)
library(ggplot2)
setwd("/media/jhuang/Elements2/Data_Anna_C.acnes/plotTreeHeatmap/")
# -- edit tree --
#https://icytree.org/
#0.000780
info <- read.csv("typing_189.csv")
info$name <- info$Isolate
#tree <- read.tree("core_gene_alignment_fasttree_directly_from_186isoaltes.tree") --> NOT GOOD!
tree <- read.tree("471.tree")
cols <- c(infection='purple2', commensalism='skyblue2')
library(dplyr)
heatmapData2 <- info %>% select(Isolate, ST, Clonal.Complex, Phylotype)
rn <- heatmapData2$Isolate
heatmapData2$Isolate <- NULL
heatmapData2 <- as.data.frame(sapply(heatmapData2, as.character))
rownames(heatmapData2) <- rn
#https://bookdown.org/hneth/ds4psy/D-3-apx-colors-basics.html
heatmap.colours <- c("cornflowerblue","darkgreen","seagreen3","tan","red", "navyblue", "gold", "green","orange","pink","purple","magenta","brown", "darksalmon","chocolate4","darkkhaki", "lightcyan3", "maroon","lightgreen", "blue","cyan", "skyblue2", "azure3","blueviolet","darkgoldenrod", "tomato","mediumpurple4","indianred",
"cornflowerblue","darkgreen","seagreen3","tan","red","green","orange","pink","brown","magenta", "cornflowerblue","darkgreen","red","tan","brown", "darkgrey")
names(heatmap.colours) <- c("1","2","3","4","5", "6","7", "20","21","22", "28","30","33","42","43","52","53", "66","68", "100","105","124","133","134","135","137", "159","161", "CC1","CC2","CC3","CC4","CC5","CC6","CC30","CC72","CC77","Singleton", "IA1","IA2","IB","II","III", "NA")
#mydat$Regulation <- factor(mydat$Regulation, levels=c("up","down"))
#circular
p <- ggtree(tree, layout='circular', branch.length='none') %<+% info +
geom_tippoint(aes(color=Type)) +
scale_color_manual(values=cols) + geom_tiplab2(aes(label=name), offset=1)
#, geom='text', align=TRUE, linetype=NA, hjust=1.8,check.overlap=TRUE, size=3.3
#difference between geom_tiplab and geom_tiplab2?
#+ theme(axis.text.x = element_text(angle = 30, vjust = 0.5)) + theme(axis.text = element_text(size = 20)) + scale_size(range = c(1, 20))
#font.size=10,
png("ggtree.png", width=1260, height=1260)
svg("ggtree.svg", width=1260, height=1260)
p
dev.off()
#png("ggtree_and_gheatmap.png", width=1290, height=1000)
#svg("ggtree_and_gheatmap.svg", width=1290, height=1000)
svg("ggtree_and_gheatmap.svg", width=17, height=15)
gheatmap(p, heatmapData2, width=0.1,colnames_position="top", colnames_angle=90, colnames_offset_y = 0.1, hjust=0.5, font.size=4, offset = 8) + scale_fill_manual(values=heatmap.colours) + theme(legend.text = element_text(size = 14)) + theme(legend.title = element_text(size = 14)) + guides(fill=guide_legend(title=""), color = guide_legend(override.aes = list(size = 5)))
dev.off()
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